GH-126920: fix Makefile overwriting sysconfig.get_config_vars

[FFY00]

• Issue: sysconfig.get_config_vars() values always get overwritten with the values from Makefile #126920

[FFY00]

I am not sure if we should backport this, as they may be users incorrectly relying on the value of sysconfig.get_config_var('prefix') or sysconfig.get_config_var('exec_prefix').

I think it's a low chance, but since this bug does not seem to be causing any known breakage in the first place, it may be worth considering leaving older versions with the incorrect value rather than breaking users possibly relying on the current value being incorrect.

3.13 is still pretty recent and people are still getting around to updating to it — in Arch Linux, for reference, we are only now starting the package rebuilds for Python 3.13 — so I don't think there'd be much harm in backporting. 3.12, tough, I am not sure.

@Yhg1s what do you think?